Senior Scientific Programmer

Department: 
HGSC:INFORMATICS-NEX GEN
Location: 
BCM Main Campus, Houston, TX
Description: 

The HGSC was founded in 1996 under the leadership of Dr. Richard Gibbs and is a world leader in genomics. The fundamental interests of the HGSC are in advancing biology and genetics by improved genome technologies. As a premier Research and Clinical Sequencing Center, the HGSC participates in the NIH’s largest genomics programs including TOPMed, the Centers for Common Disease Genomics, and All of Us. Today, the HGSC employs ~180 staff, and it occupies more than 36,000 square feet on the 14th, 15th, and 16th floors of the Margaret M. and Albert B. Alkek Building. The HGSC is located on the southwest edge of downtown Houston, the fourth largest city in the U.S., in the Texas Medical Center, the world's largest medical complex. The major activity of the HGSC is high-throughput DNA sequence generation and the accompanying analysis. The HGSC is also involved in developing the next generation of DNA sequencing and bioinformatics technologies that will allow greater scientific advances in the future.

 

This senior-level position with the Next-Generation Sequencing Informatics (NGSI) group requires a high-performing programmer and scientist with exceptional communication, organization, and time- management skills.  As the HGSC Bioinformatics Core, NGSI manages the production, maintenance and primary analysis for the HGSC’s sequencing fleet, including the HiSeq X, NovaSeq and PacBio platforms. NGSI also leads HGSC’s at-scale research informatics, specifically in the areas of structural variation and whole-genome data science. Under the direction of the Director of Genomic Informatics, an exceptionally qualified candidate will direct the research, development, deployment and maintenance of the HGSC’s structural and copy-number variant software packages and their application to large-scale research and clinical cohorts. 

 

  • Design, develop, validate and deploy production- and clinical-grade variant detection software.
  • Optimize software for local and cloud-based compute environments (AWS, Google Cloud, Azure).
  • Support all production clinical validation tests and large-scale research projects.
  • Extensive software logging, documentation and best practices.
  • Implement internal and external feature requests.
  • Continually evaluate state-of-the-art methods and incorporate into HGSC workflows.
  • Provide excellent customer service to other HGSC groups and outside collaborators

Required:

  • Bachelor's degree in Computer Science, MIS or related programming field
  • Three years experience in scientific programming.
  • Expert programmer (Python/C/C++ preferred) with at least 3 years Unix expertise
  • High-throughput execution and compute optimization in cloud environments
  • Common genomics data formats (e.g., FASTQ, BAM, VCF) 

Preferred:

  • M.S./Ph.D. in Bioinformatics, Computer Science or similar field
  • Structural and copy number variant calling methods
  • Container-based software development and Software Development Life Cycle practices
  • Next-Gen Sequencing analysis tools (e.g., BWA, vcftools, BEDtools, bamUtils, SAMtools, Picard)